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- PDB-7k2u: DHODH IN COMPLEX WITH LIGAND 13 -

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Basic information

Entry
Database: PDB / ID: 7k2u
TitleDHODH IN COMPLEX WITH LIGAND 13
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / DIHYDROOROTATE DEHYDROGENASE / DHODH / INHIBITOR
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / OROTIC ACID / TRIETHYLENE GLYCOL / Chem-VU7 / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsShaffer, P.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: A carboxylic acid isostere screen of the DHODH inhibitor Brequinar.
Authors: DeRatt, L.G. / Christine Pietsch, E. / Tanner, A. / Shaffer, P. / Jacoby, E. / Wang, W. / Kazmi, F. / Zhang, X. / Attar, R.M. / Edwards, J.P. / Kuduk, S.D.
History
DepositionSep 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,95615
Polymers39,9851
Non-polymers1,97214
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-41 kcal/mol
Surface area14950 Å2
Unit cell
Length a, b, c (Å)90.607, 90.607, 122.749
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydroorotate dehydrogenase (quinone), mitochondrial / Dihydroorotate dehydrogenase (quinone) / DHOdehase / Dihydroorotate oxidase


Mass: 39984.664 Da / Num. of mol.: 1 / Fragment: TRUNCATED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli)
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 8 types, 277 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-VU7 / 6-fluoro-2-(2'-fluoro[1,1'-biphenyl]-4-yl)-N-methoxy-3-methylquinoline-4-carboxamide


Mass: 404.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H18F2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.10 M NaAcetate pH 4.8, 2.30 M (NH4)2SO4, 30 % Glycerol, 18% (w/v) PEG 4000, 0.1M Na3Citrate pH5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.73→78.47 Å / Num. obs: 59048 / % possible obs: 96.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 28.536 Å2 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.07 / Χ2: 0.997 / Net I/σ(I): 17.96
Reflection shellResolution: 1.73→1.98 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 4.01 / Num. unique obs: 19827 / Rrim(I) all: 0.549 / % possible all: 98.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.73→78.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.179 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0805 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2914 4.9 %RANDOM
Rwork0.1649 ---
obs0.1656 56134 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.64 Å2 / Biso mean: 26.958 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.73→78.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 136 269 3201
Biso mean--35.89 38.13 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0113016
X-RAY DIFFRACTIONr_bond_other_d0.0042927
X-RAY DIFFRACTIONr_angle_refined_deg1.5534086
X-RAY DIFFRACTIONr_angle_other_deg1.2956707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.026129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.878497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.36530
X-RAY DIFFRACTIONr_chiral_restr0.088452
X-RAY DIFFRACTIONr_gen_planes_refined0.0073421
X-RAY DIFFRACTIONr_gen_planes_other0.003672
LS refinement shellResolution: 1.73→1.775 Å
RfactorNum. reflection% reflection
Rfree0.315 181 -
Rwork0.308 4273 -
obs--98.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7610.11750.76251.9411-0.79773.3774-0.0774-0.27880.15380.21950.023-0.2904-0.20160.39280.05440.1739-0.0513-0.05520.1181-0.04910.0932-22.97123.57424.856
20.36390.1432-0.04411.5514-0.54251.5576-0.04960.07470.016-0.12240.02560.02220.0024-0.02210.02390.045-0.02060.00130.02150.00090.0026-34.4914.8457.712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 70
2X-RAY DIFFRACTION2A71 - 396

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